Abstract The Namib Desert is a hyperarid coastal desert where fog is a major moisture source. We hypothesized that the fog-harvesting grass Stipagrostis sabulicola establishes an important ecological ...niche, termed the "Fog-Plant-Oases" (FPOs), and serves as the primary carbon source for the invertebrate community. To determine this, we measured the natural variations of the stable carbon and nitrogen isotopes (δ 13 C and δ 15 N) of invertebrates as well as that of plant biomass and belowground detritus and estimated the contributions of the fog plants in their diets. Our findings revealed a complex trophic structure and demonstrated that S. sabulicola fuels carbon flow from lower to higher trophic levels in the aboveground food web. The distinct δ 13 C values of bacterial- and fungal-feeding nematodes indicated however the separation of the aboveground niche, which is primarily sustained by S. sabulicola , from the belowground niche, where wind-blown sediments may serve as the main energy source for the soil biota. Our findings further accentuate the critical role of S. sabulicola FPOs in establishing complex trophic dynamics and a distinctive food web within the hyperarid Namib dunes.
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•Phylogenetic position of the most enigmatic clawless eutardigrade genus Apodibius was resolved.•The type species of the genus Apodibius, A. confusus, reconstructed within ...Isohypsibioidea.•Apodibius confusus is a member of the clade grouping Isohypsibius asper, I. granulifer, and Eremobiotus alicatai.•The genus Isohypsibius is an artificial paraphyletic taxon.•Novel sequence data for the eutardigrade 18S and 28S rRNA genes are published.
The systematics of Eutardigrada, the largest lineage among the three classes of the phylum Tardigrada, is based mainly on the morphology of the leg claws and of the buccal apparatus. However, three members of the rarely recorded and poorly known limno-terrestrial eutardigrade genus Apodibius have no claws on their strongly reduced legs, a unique character among all tardigrades. This absence of all claws makes the systematic position of Apodibius one of the most enigmatic among the whole class. Until now all known associates of the genus Apodibius have been located in the incertae sedis species group or, quite recently, included into the Necopinatidae family. In the present study, phylogenetic analyses of 18S and 28S rRNA sequence data from 31 tardigrade species representing four parachelan superfamilies (Isohypsibioidea, Hypsibioidea, Macrobiotoidea, Eohypsibioidea), the apochelan Milnesium tardigradum, and the type species of the genus Apodibius, A. confusus, indicated close relationship of the Apodibius with tardigrade species recently included in the superfamily Isohypsibioidea. This result was well-supported and consistent across all markers (separate 18S rRNA, 28S rRNA, and combined 18S rRNA+28S rRNA datasets) and methods (MP, ML) applied.
Metagenomics – shotgun sequencing of all DNA fragments from a community DNA extract – is routinely used to describe the composition, structure, and function of microorganism communities. Advances in ...DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene‐based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.
We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.
We recovered over 95% of the species, and observed relatively high false‐positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon‐specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass–read relationships. Results were similar among different sequencing efforts.
The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low‐ and high‐sequencing efforts yield similar results, suggesting high cost‐efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics‐based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.
Shotgun metagenomics is increasingly applicable to study eukaryotic community composition. Theoretically, metagenomics should inform about species’ biomass, since it omits a taxonomically biased PCR step. Here, we evaluate how well metagenomics records composition and biomass in mock communities, and how its performance is affected by reference genome properties.
In an afforested coal-mining site at Berzdorf, Germany, the soil tardigrade community was investigated. Tardigrade densities ranged from 300 to 33,600 individuals
m
−2. Tardigrade distribution was ...very aggregated with standard deviations of up to 220% of mean densities. Fourteen species belonging to five eutardigrade genera were identified. Soils were dominated by the carnivorous tardigrade
Macrobiotus richtersi that contributed 60% of overall densities. A comparison between nine soils of different forest ages (4–46 years) and tree species (poplar, alder, pine, mixed deciduous and mixed coniferous) showed no relationship of tardigrade species distribution and abundance to tree species, thickness of organic or litter layer, humus form, pH or soil moisture. Further, no correlation between nematode biomass and
Macrobiotus richtersi abundances were detected. The age of afforested soils, however, affected tardigrade densities: younger soils (7–17 years) yielded higher tardigrade numbers compared to 46-year-old sites.
Life history investigations on a strain of parthenogenetic
Macrobiotus richtersi demonstrated a significant influence of temperature on egg development, survival rate, body growth and generation time. Hatching, first to fourth molts and maturing, on the other hand, were dependent upon body size alone. The simple, new culture method for carnivorous tardigrades described has successfully been utilized for parthenogenetic
Macrobiotus richtersi for 6 years.
We investigated foraging behavior of a carnivorous eutardigrade, Macrobiotus richtersi, living in soil or fresh water sediments, where the distribution of nematode prey is heterogeneous and where, ...consequently, the value of information about prey availability should be high. We directly observed diet choice in various mixtures of 2 size classes of nematodes Acrobeloides nanus, A1 (small prey) and A2 (large prey), differing in profitability (biomass divided by handling time) but not in digestive quality. At various prey densities of A2, we measured how much of each prey item was consumed as a function of search time. Additionally, we derived cumulative biomass uptake rates per single A2 prey from 154 complete feeding acts, and we used the marginal value theorem (MVT) to predict optimal residence time and prey exploitation as a function of environmental quality and search time. Macrobiotus richtersi did not preferentially select the more profitable size class A2 but increased its biomass uptake rate by modifying the amount consumed per prey item (partial consumption): when encounter rates were high and there were more high-quality prey, the tardigrade abandoned food more quickly and consumed less biomass per captured prey. We conclude that 1) hungry tardigrades under food-rich or food-limited conditions maximize biomass gain according to MVT and 2) tardigrades differentiate at least 2 prey situations, high supply (at high encounter rates) and low supply (at moderate and low prey densities). 3) Partial consumption, performed under food-rich conditions or by a satiated predator, leads to a reduction of prey numbers up to 3 times as much as under food-poor conditions.
In a series of laboratory experiments, we presented carnivorous Macrobiotus richtersi (Tardigrada, Macrobiotidae) with nematode prey to assess their importance as predator. We investigated ...consumption rate for (a) different prey densities (10-400 prey individuals), (b) different prey biomasses (22-80 ng), (c) different prey species (Pelodera teres, Rhabditidae, versus Acrobeloides nanus, Cephalobidae) and (d) different environments (2-D agar surface versus 3-D sand fractions of three different textures). M. richtersi consumed up to 4.6 micrograms nematode prey in 4 h, that is, 43% of the tardigrades body mass. Predation rate was positively correlated with prey density. The optimal prey in the present investigation was the biggest prey because it yielded the highest biomass uptake per time. In addition, the size of M. richtersi played an important role in consumption rate. Bacterivorous nematodes reacted differently to attack. Even in a water film on stiff agar where nematode agility was limited, a vigorous undulation reaction of P. teres led to a measurable reduction in consumption rate. A. nanus, in contrast, showed little response to attack. Microcosm experiments with sands of different particle size demonstrated that M. richtersi is able to chase and consume small bacterivorous nematodes in a 3-D soil matrix. However, consumption rate in sand microcosms was significantly reduced compared with pure agar. The sand matrix improved nematode agility and possibly provided small pores as refuge for the nematodes. The lowest consumption rate was observed in fine sand. Effects of predatory tardigrades on nematode numbers in the field are discussed.
Abstract
The present study gives the first detailed results on the partner-finding behaviour of tardigrades. We investigated whether the finding of mating partners by Isohypsibius dastychi followed ...certain criteria that are expected if pheromone signals are involved. For this purpose, tardigrade pairs were positioned in an arena, at a range of distances from each other. Only those females that were ready for mating attracted the male. The smaller the initial distance between them, the more directly the male headed for the female. The route travelled and time taken increased exponentially with increasing initial distance between partners, which means that the male lost orientation with respect to the female the larger the distance between the pair became. The findings indirectly suggest a yet undetermined female pheromone, which produces a concentration gradient in the water and loses strength quickly in terms of distance. Our assumption is supported by rare observations of sperm release without direct contact between partners that nevertheless resulted in fertile offspring. The observation that the female partners in this no-contact mating behaviour then deposited their eggs (a behaviour that was never seen when males were absent) suggests that they, likewise, can sense a fresh ejaculate of spermatozoa in their direct vicinity.
Soil invertebrates are among the least understood metazoans on Earth. Thus far, the lack of taxonomically broad and dense genomic resources has made it hard to thoroughly investigate their evolution ...and ecology. With MetaInvert we provide draft genome assemblies for 232 soil invertebrate species, representing 14 common groups and 94 families. We show that this data substantially extends the taxonomic scope of DNA- or RNA-based taxonomic identification. Moreover, we confirm that theories of genome evolution cannot be generalised across evolutionarily distinct invertebrate groups. The soil invertebrate genomes presented here will support the management of soil biodiversity through molecular monitoring of community composition and function, and the discovery of evolutionary adaptations to the challenges of soil conditions.
This study focuses on the CO2-tolerance of soil nematodes from natural CO2 springs (mofette fields). In laboratory experiments, we compared survival, reproduction, activity and reactivation of a ...CO2-sensitive species with a CO2-tolerant species. Both species survived even 100% CO2, but in an inactive state. The higher the CO2 concentration the more individuals entered inactivity. We found significant differences between the two species: more adults of the CO2-tolerant species maintained activity and reproduction at higher CO2 concentrations. Moreover, reactivation after inactivity was faster. Together with a higher juvenile mortality of the CO2-sensitive species, these interspecific differences are conclusive to explain the niche separation of the two species that was observed in the mofette field.
•We tested survival and activity of 2 nematode species from natural CO2 springs.•From their distribution in the field, one species is CO2-tolerant, one CO2-sensitive.•In the lab, adults of both species survived 5 days at 100% CO2 in an inactive state.•The CO2-tolerant species maintains activity and reproduction at higher CO2 levels.•Our results explain the niche separation of the two species observed in the field.
Phylogenetic positioning within Eutardigrada is based mainly on claw and buccopharyngeal morphology. In tardigrades that lack claws, i.e. representatives of the genus Apodibius, buccopharyngeal ...structures are the only morphological characters used for systematic classification. Investigating the feeding apparatus of Apodibius confusus Dastych, with light microscopy and scanning electron microscopy (SEM) techniques, the present study added morphological affirmation to the recently published molecular classification of A. confusus as a representative of Isohypsibiidae. The present study aimed to disentangle which of the Isohypsibiidae genera A. confusus is most closely related to. From a morphological point of view and with the SEM images presently available, A. confusus appears closest to Hexapodibius and Doryphoribius. The present study once more revealed the need for investigations that combine molecular and detailed morphological data to finally disentangle the phylogeny of Isohypsibiidae.
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